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    <title>Visualization - Peak list table</title>
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<h1>Peak list table</h1>

<h2>Description</h2>

<p>
    This shows a list of identified peaks, after applying a series of methods to a raw data. This feature is one of the
    most important of MZmine project, because collect the result of many other modules.
</p>

<p>
    The table is divided in many columns, which the user can edit which columns to show in the peak list.
</p>

<h3>Columns</h3>

<p>
    The columns can be divided by two groups "Common" and "Data file". The first group shows a collective information
    that represents the peak row. The second group displays the information of each particular peak in the row.
</p>

<h4>Common</h4>

<dl>
    <dt>ID</dt>
    <dd>This is the number that identify the row peak. A row peak can contain one or many peaks that share the same mass
        range and retention time range but coming from different raw data.
    </dd>

    <dt>m/z</dt>
    <dd>This is the representative m/z value for this row peak (average of all peak's m/z value). The m/z value of each
        peak depends on the peak identification method. Please refer to "Peak detection" section of this help
    </dd>

    <dt>Ret.time</dt>
    <dd>This is the representative retention time value for this row peak (average of all peak's ret. time value). The
        ret. time value of each peak depends on the used peak identification method. Please refer to "Peak detection"
        section of this help
    </dd>

    <dt>Identity</dt>
    <dd>This is the name, assigned from the peak's identity. This value depends on the method to identify the peak.
        Please refer to "Identification" section of this help.
    </dd>

    <dt>Comment</dt>
    <dd>This is an user input value. It can be edited by making double click.</dd>

    <dt>Peak shape</dt>
    <dd>This is graphic representation of the peaks in two axis (X - retention time, Y-intensity) with a different color
        for each peak in the row. The size of this graphic can be edited.
    </dd>
</dl>

<h4>Data file</h4>

<dl>
    <dt>Status</dt>
    <dd>A circle of different color will appear indicating the status of the peak. The meaning of the color is as
        follow, RED = no detected, ORANGE= manually detected by the user, YELLOW = detected by the "Gap Filler" tool and
        GREEN = detected.
    </dd>

    <dt>Peak shape</dt>
    <dd>This is graphic representation of the peaks in two axis (X - retention time, Y-intensity), in this case a XIC
    </dd>

    <dt>m/z</dt>
    <dd>The m/z value of the peak and depends on the peak identification method. Please refer to "Peak detection"
        section of this help.
    </dd>

    <dt>Ret.time</dt>
    <dd>The ret. time value of the peak and depends on the used peak identification method. Please refer to "Peak
        detection" section of this help
    </dd>

    <dt>Duration</dt>
    <dd>The duration of the peak on terms of time.</dd>

    <dt>Height</dt>
    <dd>The intensity of the peak in his highest point.</dd>

    <dt>Area</dt>
    <dd>The calculated area of the peak using the intensity and the duration of the peak.</dd>

    <dt>Charge</dt>
    <dd>The value of the ion charge. This value is obtained from the raw data or by the Isotope grouper module</dd>

</dl>

<h4>Functionality</h4>

<p>
    This table offers the possibility to sort the rows by some of the columns by making click on the header of each
    column.
</p>

<p>
    <img src="Peaklist_table1.png">
</p>

<p>
    The tool bar at the right side of the table the user can edit the columns to display on the table and to print the
    displayed information.
</p>

<p>
    <img src="Peaklist_table_properties.png">
</p>

<p>
    Each column has his a tool tip that provides some extra information. The contents of the tool tip box in the column
    identity depends on the applied method to identified the peak. Please refer to the "Identification" section of
    this help. This tool tip appears automatically when passing over the mouse.
</p>

<p>
    <img src="Peaklist_table_tooltip1.png">
    <img src="Peaklist_table_tooltip2.png">
    <img src="Peaklist_table_tooltip3.png">
</p>

<h4>Submenu</h4>

<p>
    A pop-up menu will appear if right click is done. Some of the options in this menu are active depending on the
    position (column) where the click is done and the number of selected rows.
</p>

<dl>
    <dt>Show</dt>
    <dd>Under this option appear other submenu from where the user can choose the any visualization plot available for
        this peak. Some of the options depends on the characteristics of the selected row or peak. For more information
        about each kind of visualization refer to the "Visualization" section of this help.
    </dd>

    <dt>Search</dt>
    <dd>This sub-menu holds items for searching on-line databases, performing a NIST MS Search and formula prediction.
    </dd>

    <dt>Plot using Intensity Plot module</dt>
    <dd>An intensity plot will be formed using the selected peaks. Please refer to "Visualization - Intensity plot"
        section of this help.
    </dd>

    <dt>Manually define peak</dt>
    <dd>The user can define manually the range of m/z and retention time of a peak. MZmine will create a new one or
        modify an existing peak.
    </dd>

    <dt>Clear selected rows’ identities</dt>
    <dd>Removes the identities from the selected peaks.</dd>

    <dt>Delete selected rows</dt>
    <dd>The selected rows will be removed from the peak list. There is no way to recover the deleted rows.</dd>

    <dt>Add new row</dt>
    <dd>The same functionality as Manually define peak, but applied to all the raw data files in the peak list. At the
        end, the result is a new row with peaks from all the raw data files using the input ranges by the user.
    </dd>
</dl>

<p>
    <img src="Peaklist_table_submenu.png">
</p>

<p>
    For the Identity column, a specific submenu will appear with left click. This submenu has the options to choose or
    edit the active identity from many associated to the same peak,
</p>

<p>
    <img src="Peaklist_table_submenu_ident.png">
</p>

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